calcCs: Calculates the C1-C4 measures of convergent evolution between...
In convevol: Analysis of Convergent Evolution
calcCs R Documentation
Calculates the C1-C4 measures of convergent evolution between two lineages as described in
Stayton (2015). All measures quantify convergence by the ratio of current to maximum past phenotypic
distance between lineages. Can be used as-is but more often will be used within the calcConv script.
Code written by Jonathan S. Mitchell for Zelditch et al. (2017)
Description
calcCs calculates the C1-C4 measures of convergent evolution
Usage
calcCs(tips, ancList, allDists, phy, VERBOSE = FALSE)
Arguments
tips
Two putatively convergent tips
ancList
A list of ancestors of all tips. Most often obtained from calcConv
allDists
A matrix of phenotypic distances between all nodes (tips and ancestors). Most often
obtained from calcConv
phy
The phylogeny of interest
VERBOSE
Whether or not to print progress
Details
calcCs calculates values of C1-C4, all of which are fundamentally based on comparing the
current phenotypic distance between two tips to the maximum past distances between the ancestors of
those tips. Higher values indicate a greater amount of past phenotypic distance which has been "closed"
by subsequent evolution, and thus greater convergence. C1 is the ratio of tip to maximum ancestral
distance. C2 is the difference of those two values. C3 scales C2 by the total amount of evolution that
has occured in the two lineages. C4 scales C2 by the total amount of evolution that has occurred in the
entire phylogeny. The arguments for this function will usually be obtained from the calcConv script in
convevol - this allows certain computationally-intensive steps (e.g., calculating ancestral states) to
only be performed once, thus saving a great deal of time. This script also corrects an error in the
calculation of C4 of previous versions of convevol.
Value
C1-C4 convergence measures for all pairs of putatively convergent taxa.
References
Stayton, C.T. 2015. The definition, recognition, and interpretation of convergent evolution, and
two new measures for quantifying and assessing the significance of convergence. Evolution 69:2140-2453.
Zelditch, M.L., J. Ye, J.S. Mitchell, and D.L. Swiderski. 2017. Rare ecomorphological
convergence on a complex adaptive landscape: Body size and diet mediate evolution of jaw shape in
squirrels (Sciuridae). Evolution 71:633-649.
convevol documentation built on July 9, 2023, 5:07 p.m.
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| calcCs | R Documentation |
Calculates the C1-C4 measures of convergent evolution between two lineages as described in Stayton (2015). All measures quantify convergence by the ratio of current to maximum past phenotypic distance between lineages. Can be used as-is but more often will be used within the calcConv script. Code written by Jonathan S. Mitchell for Zelditch et al. (2017)
Description
calcCs calculates the C1-C4 measures of convergent evolution
Usage
calcCs(tips, ancList, allDists, phy, VERBOSE = FALSE)
Arguments
tips |
Two putatively convergent tips |
ancList |
A list of ancestors of all tips. Most often obtained from calcConv |
allDists |
A matrix of phenotypic distances between all nodes (tips and ancestors). Most often obtained from calcConv |
phy |
The phylogeny of interest |
VERBOSE |
Whether or not to print progress |
Details
calcCs calculates values of C1-C4, all of which are fundamentally based on comparing the current phenotypic distance between two tips to the maximum past distances between the ancestors of those tips. Higher values indicate a greater amount of past phenotypic distance which has been "closed" by subsequent evolution, and thus greater convergence. C1 is the ratio of tip to maximum ancestral distance. C2 is the difference of those two values. C3 scales C2 by the total amount of evolution that has occured in the two lineages. C4 scales C2 by the total amount of evolution that has occurred in the entire phylogeny. The arguments for this function will usually be obtained from the calcConv script in convevol - this allows certain computationally-intensive steps (e.g., calculating ancestral states) to only be performed once, thus saving a great deal of time. This script also corrects an error in the calculation of C4 of previous versions of convevol.
Value
C1-C4 convergence measures for all pairs of putatively convergent taxa.
References
Stayton, C.T. 2015. The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence. Evolution 69:2140-2453.
Zelditch, M.L., J. Ye, J.S. Mitchell, and D.L. Swiderski. 2017. Rare ecomorphological convergence on a complex adaptive landscape: Body size and diet mediate evolution of jaw shape in squirrels (Sciuridae). Evolution 71:633-649.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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